Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate 7024550 Shewana3_1728 succinylarginine dihydrolase (RefSeq)
Query= reanno::ANA3:7024550 (444 letters) >FitnessBrowser__ANA3:7024550 Length = 444 Score = 895 bits (2314), Expect = 0.0 Identities = 444/444 (100%), Positives = 444/444 (100%) Query: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60 MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG Sbjct: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60 Query: 61 MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120 MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT Sbjct: 61 MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120 Query: 121 RDGKLHFTPANLVDKLHRSIEPTTTGRILTATFNDPHYFHHHNHLPEHNSFGDEGAANHT 180 RDGKLHFTPANLVDKLHRSIEPTTTGRILTATFNDPHYFHHHNHLPEHNSFGDEGAANHT Sbjct: 121 RDGKLHFTPANLVDKLHRSIEPTTTGRILTATFNDPHYFHHHNHLPEHNSFGDEGAANHT 180 Query: 181 RLCQEYGHAGVELFVYGQEATNPNAPRPQKYPARQTLEASMAIARLHQLEEDNCVFIQQN 240 RLCQEYGHAGVELFVYGQEATNPNAPRPQKYPARQTLEASMAIARLHQLEEDNCVFIQQN Sbjct: 181 RLCQEYGHAGVELFVYGQEATNPNAPRPQKYPARQTLEASMAIARLHQLEEDNCVFIQQN 240 Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIRRKLDTELFFIEVPTTKVAIN 300 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIRRKLDTELFFIEVPTTKVAIN Sbjct: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIRRKLDTELFFIEVPTTKVAIN 300 Query: 301 NAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLTLNTPIKQVLYFDVKQSM 360 NAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLTLNTPIKQVLYFDVKQSM Sbjct: 301 NAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLTLNTPIKQVLYFDVKQSM 360 Query: 361 QNGGGPACLRLRVAMNEREVAAANQHTLLNDALFARLNTWVDKHYRDRLSTQDLADPQLV 420 QNGGGPACLRLRVAMNEREVAAANQHTLLNDALFARLNTWVDKHYRDRLSTQDLADPQLV Sbjct: 361 QNGGGPACLRLRVAMNEREVAAANQHTLLNDALFARLNTWVDKHYRDRLSTQDLADPQLV 420 Query: 421 VESRTALDELTQIMKLGSVYPFQR 444 VESRTALDELTQIMKLGSVYPFQR Sbjct: 421 VESRTALDELTQIMKLGSVYPFQR 444 Lambda K H 0.318 0.132 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 816 Number of extensions: 13 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 444 Length adjustment: 32 Effective length of query: 412 Effective length of database: 412 Effective search space: 169744 Effective search space used: 169744 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate 7024550 Shewana3_1728 (succinylarginine dihydrolase (RefSeq))
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03241.hmm # target sequence database: /tmp/gapView.1619.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03241 [M=443] Accession: TIGR03241 Description: arg_catab_astB: succinylarginine dihydrolase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-225 735.4 1.5 1.4e-225 735.3 1.5 1.0 1 lcl|FitnessBrowser__ANA3:7024550 Shewana3_1728 succinylarginine d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024550 Shewana3_1728 succinylarginine dihydrolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 735.3 1.5 1.4e-225 1.4e-225 2 443 .] 4 443 .. 3 443 .. 0.99 Alignments for each domain: == domain 1 score: 735.3 bits; conditional E-value: 1.4e-225 TIGR03241 2 yevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklGfsG 78 +e+nfdGlvG+thnyaGlsfGn+as +n vsnpk+aakqGl+k kaladlG+ qg+lapqerpd+++lr++GfsG lcl|FitnessBrowser__ANA3:7024550 4 FEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQGMLAPQERPDLNTLRRIGFSG 80 8**************************************************************************** PP TIGR03241 79 sdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkaifadek 155 sd++vl++aa++ap ll a +sassmwtanaatvspsadt dg++hft+anl k+hrsie tt r+l+a+f+d + lcl|FitnessBrowser__ANA3:7024550 81 SDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADTRDGKLHFTPANLVDKLHRSIEPTTTGRILTATFNDPH 157 ***************************************************************************** PP TIGR03241 156 kfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlhqleeekv 231 +f +h+ lp+++++GdeGaanhtrl++ey+++gvelfvyG++a ++p+p++yparqtleas a+arlhqlee++ lcl|FitnessBrowser__ANA3:7024550 158 YFHHHNHLPEHNSFGDEGAANHTRLCQEYGHAGVELFVYGQEATnPNAPRPQKYPARQTLEASMAIARLHQLEEDNC 234 ******************************************997899***************************** PP TIGR03241 232 vyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylf 308 v++qqnpdvidqGvfhndviav+n++vlf+he+afln+++ lde+r+kl++ l ievp+++v++++av+sylf lcl|FitnessBrowser__ANA3:7024550 235 VFIQQNPDVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIRRKLDTE---LFFIEVPTTKVAINNAVKSYLF 308 ************************************************9876...99******************** PP TIGR03241 309 nsqllskedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnp 385 n+q+++ g+m ++ p +c+en+av+ayl+el++ ++pik+v fd+++sm+nGGGpaclrlrv++n+ e+aa n+ lcl|FitnessBrowser__ANA3:7024550 309 NTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLTLNTPIKQVLYFDVKQSMQNGGGPACLRLRVAMNEREVAAANQ 385 ***************************************************************************** PP TIGR03241 386 kvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443 ++ll+dalfa+ln+wvd+hyrdrls++dladpql+vesrtaldeltqi++lGsvy+fq lcl|FitnessBrowser__ANA3:7024550 386 HTLLNDALFARLNTWVDKHYRDRLSTQDLADPQLVVESRTALDELTQIMKLGSVYPFQ 443 *********************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (444 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.79 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory